Fix filter tables (scverse#619)

* fix filter_tables

* add test

* add fix to changelog

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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---------

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CHANGELOG.md

@@ -14,7 +14,7 @@ and this project adheres to [Semantic Versioning][].
 
 ### Minor
 
--  Relaxing `spatial-image` package requirement #616
+-   Relaxing `spatial-image` package requirement #616
 
 ## [0.2.0] - 2024-07-03
 
@@ -43,6 +43,7 @@ and this project adheres to [Semantic Versioning][].
 ### Fixed
 
 -   Preserve channel names of multi-scale images in `transform` (#379)
+-   Fix `filter_by_coordinate_system` with SpatialData object having a table not annotating an element (#619)
 
 ## [0.1.2] - 2024-03-30
 

src/spatialdata/_core/spatialdata.py

@@ -722,6 +722,8 @@ def _filter_tables(
                 if include_orphan_tables and not table.uns.get(TableModel.ATTRS_KEY):
                     tables[table_name] = table
                     continue
+                if not include_orphan_tables and not table.uns.get(TableModel.ATTRS_KEY):
+                    continue
                 if table_name in names_tables_to_keep:
                     tables[table_name] = table
                     continue

tests/core/query/test_relational_query.py

@@ -684,6 +684,14 @@ def test_filter_table_categorical_bug(shapes):
     shapes.filter_by_coordinate_system("global")
 
 
+def test_filter_table_non_annotating(full_sdata):
+    obs = pd.DataFrame({"test": ["a", "b", "c"]})
+    adata = AnnData(obs=obs)
+    table = TableModel.parse(adata)
+    full_sdata["table"] = table
+    full_sdata.filter_by_coordinate_system("global")
+
+
 def test_labels_table_joins(full_sdata):
     element_dict, table = join_spatialelement_table(
         sdata=full_sdata,